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- PDB-5c3d: Crystal structure of ABBB + UDP-C-Gal (short soak) + DI -

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Basic information

Entry
Database: PDB / ID: 5c3d
TitleCrystal structure of ABBB + UDP-C-Gal (short soak) + DI
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / Glycosyltransferase Deoxyinhibitor ABO(H) Blood-Group System Complex
Function / homology
Function and homology information


fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region
Similarity search - Function
Glycosyl transferase, family 6 / Glycosyltransferase family 6 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Chem-URM / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsGagnon, S. / Meloncelli, P. / Zheng, R.B. / Haji-Ghassemi, O. / Johal, A.R. / Borisova, S. / Lowary, T.L. / Evans, S.V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-77655 Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: High Resolution Structures of the Human ABO(H) Blood Group Enzymes in Complex with Donor Analogs Reveal That the Enzymes Utilize Multiple Donor Conformations to Bind Substrates in a Stepwise Manner.
Authors: Gagnon, S.M. / Meloncelli, P.J. / Zheng, R.B. / Haji-Ghassemi, O. / Johal, A.R. / Borisova, S.N. / Lowary, T.L. / Evans, S.V.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.source / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4964
Polymers34,7561
Non-polymers7393
Water4,468248
1
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9918
Polymers69,5122
Non-polymers1,4796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area5860 Å2
ΔGint-30 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.540, 149.770, 79.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histo-blood group ABO system transferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N- ...Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Histo-blood group A transferase / A transferase / Histo-blood group B transferase / B transferase / NAGAT


Mass: 34756.098 Da / Num. of mol.: 1 / Fragment: UNP residues 64-354 / Mutation: G235S, L266M, G268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli)
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Chemical ChemComp-URM / (((2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)methyl)phosphonic (((2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride / Uridine diphospho methylene galactopyranose


Mass: 564.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Grown in 1% polyethylene glycol (PEG) 4000, 4.5-5% 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM N-[-acetamido]-2-iminodiacetic acid (ADA), 30 mM ...Details: Grown in 1% polyethylene glycol (PEG) 4000, 4.5-5% 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM N-[-acetamido]-2-iminodiacetic acid (ADA), 30 mM sodium acetate, 5 mM manganese chloride. Grown 5-10 days.

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.39→74.95 Å / Num. obs: 60710 / % possible obs: 96 % / Redundancy: 4.05 % / Rmerge(I) obs: 0.03 / Χ2: 1.01 / Net I/σ(I): 24.1 / Num. measured all: 247943 / Scaling rejects: 1860
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.39-1.442.050.28631113954321.03587
1.44-1.53.320.2594.12034261161.083297.3
1.5-1.573.590.2275.12204961161.117298.5
1.57-1.653.760.1896.12341062001.0911698.4
1.65-1.753.990.1517.82485461861.0617698.8
1.75-1.894.440.09811.92782462150.9625098.7
1.89-2.084.570.05220.92854761900.9627898.3
2.08-2.384.750.036302953661640.9626597.4
2.38-2.994.870.024443001961130.9325795.7
2.99-19.824.990.015763022359780.9940990.6

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Processing

Software
NameVersionClassification
d*TREK9.4SSIdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
CrystalClear1.3.6 SP2 r1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LZ7

1lz7


Resolution: 1.39→74.95 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.949 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 3085 5.1 %RANDOM
Rwork0.1973 ---
obs0.1981 57622 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.5 Å2 / Biso mean: 19.426 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.39→74.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 44 248 2542
Biso mean--23.34 28.72 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192387
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9693251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3735282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48922.818110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1715387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5821518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211806
X-RAY DIFFRACTIONr_mcbond_it1.0041.7571124
X-RAY DIFFRACTIONr_mcangle_it1.622.6291408
X-RAY DIFFRACTIONr_scbond_it1.5481.9191262
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 210 -
Rwork0.473 3658 -
all-3868 -
obs--83.89 %

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